Fixes and enhancements for nf annotation utils

[anngvu]

Some more fixes an enhancements to note:

• It seems it is possible for samtools to not have a row for an outputted bam, so should use a left join when merging data so a bam file is not missing in the generated manifest.
• The API/approach CNVkit for annotate_cnv is actually pretty different than from annotate_called_variants or annotate_expression when it doesn't have to be, mostly bc it was written a year after the first two. But anyone trying to use annotate_cnv with one of the other two at the same time will likely be a little thrown off by the different implementations. Ergo, this should be rewritten to resolve inconsistencies.
• Do more automatic detection/extraction of workflow meta instead of users having to input certain ids or labels.
• Ensure pipe-able expressions.

This is clustered with #182, #178, #55 and can take into account one or more of those issues so the refactor synergizes resolution with these other issues / makes it easier to resolve these other issues. Alongside the work on other issues, this should yield and overall faster, more thorough, more intuitive, and more consistent set of annotation utilities.